Abstract

Abstract Motivation Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains >67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims to identify and categorize these small molecules in the PDB and make it easier to find them. Results The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process. Availability and implementation Information is made available on the individual PDBe entry pages at pdbe.org and programmatically through the PDBe REST API (pdbe.org/api). Supplementary information Supplementary data are available at Bioinformatics online.

Keywords

CofactorProtein Data Bank (RCSB PDB)Protein Data BankPipeline (software)EnzymeComputer scienceBiochemistryComputational biologyChemistryProtein structureBiologyProgramming language

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Publication Info

Year
2019
Type
article
Volume
35
Issue
18
Pages
3510-3511
Citations
31
Access
Closed

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Cite This

Abhik Mukhopadhyay, Neera Borkakoti, Lukáš Pravda et al. (2019). Finding enzyme cofactors in Protein Data Bank. Bioinformatics , 35 (18) , 3510-3511. https://doi.org/10.1093/bioinformatics/btz115

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DOI
10.1093/bioinformatics/btz115